Cancer Bioinformatics Infrastructure Objects (caBIO)
Conducting biomedical research requires access to experimental data, as well as associated molecular annotations. Annotations providing detailed information on the molecular origin, biological process, and genetic alterations can provide important insight on experimental outcomes. caBIO (cancer Bioinformatics Infrastructure Objects) is a robust resource for accessing molecular annotations from curated data sources in an integrated view in support of knowledge discovery.
The caBIO domain model and architecture is an ongoing effort to model the rapidly-changing genomics and proteomics domain and to integrate data from numerous sources providing a holistic view of the human and mouse genomes. The entities that concern the Central Dogma of Molecular Biology are the core of the model. The integration of genome annotations with clinical trials, pathway, and literature associations allows researchers to discover associations in the data that were previously unseen in the separate datasets thereby enhancing cancer research and drug design. In caBIO, information is modeled as close to the corresponding biological entities as possible to enable better usability for researchers and application developers alike.
Data for the classes come from a variety of sources, including CGAP, Unigene, the Cancer Gene Index (CGI) project, the Pathway Interaction Database (PID), as well as a number of array manufacturers (for microarray annotations). Given the dynamic nature of this information, the data in caBIO is updated semi-monthly through a series of ETL (Extract, Transform and Load) processes.
Access to this data is provided through a variety of interfaces, including a remote Java API; web services (SOAP and REST API); grid data services available on caGrid; and graphical user interfaces (GUIs) including a caBIO web page and caBIO Portlet available through the caGrid Portal. GUI tools allow researchers to perform a Google ™-like FreestyleLM search that provides end-users with a simple interface to readily browse the contents of the repository. Template-based searches are also available via the caBIO Portlet, allowing researchers to execute common queries based on pre-defined templates.
Intended AudiencesBiomedical Informaticians
Tool Download Files
Domain and Technical Information